Mediator regulates transcriptional termination through crosstalk with pre-mRNA 3' end processing factors

Beyond its function in transcription initiation, the Mediator complex coordinates the processes of transcription elongation and mRNA splicing. Here, we report that Mediator associates with the cleavage and polyadenylation specificity factor (CPSF) complex in the pre-mRNA 3' end processing machinery, partially through the MED23-FIP1 connection, for control of transcription termination in human cells. We observed the physical association and coordinated occupancy of MED23 and FIP1 at both promoter and terminator regions and found that MED23 directly binds to hundreds of 3' mRNAs. Depleting MED23 or FIP1 or overexpressing the intrinsically disordered regions (IDRs) of FIP1 compromised the Mediator-CPSF association and reduced the genomic occupancy of CPSF. Consequently, MED23 deficiency led to hundreds of readthrough events and fusion transcripts, and the 3' RNA binding of MED23 is critical for the transcription termination regulation. Moreover, integrative analysis revealed that MED23 deficiency contributed to readthrough events in breast cancers, thus providing critical molecular insights into carcinogenesis.